Slide rack determination system

ABSTRACT

A slide rack determination system for a digital slide scanning apparatus. In an embodiment, a motor drives a slide rack at a known rate toward an engagement surface. The elapsed time until engagement may be used to detect the presence or absence of the slide rack and/or the height of the slide rack. In addition, one or more sensors may detect one or more features of the slide rack, and these feature(s) may be used to determine the presence or absence of a slide rack, whether usage of the slide rack is supported or unsupported by the digital slide scanning apparatus, the orientation of the slide rack, and/or the manufacturer and/or model of the slide rack.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Patent App. No.62/591,103, filed on Nov. 27, 2017, which is hereby incorporated hereinby reference as if set forth in full.

BACKGROUND Field of the Invention

The present invention relates generally to a digital slide scanningapparatus (e.g. for pathology), and, more particularly, to a system fordetermining a type (e.g., manufacturer, model, etc.) and/or orientationof a slide rack, prior to the scanning of individual glass slides by adigital slide scanning apparatus.

Related Art

Digital pathology is an image-based information environment which isenabled by computer technology that allows for the management ofinformation generated from a physical slide. Digital pathology isenabled in part by virtual microscopy, which is the practice of scanninga specimen on a physical glass slide and creating a digital slide imagethat can be stored, viewed, managed, and analyzed on a computer monitor.With the capability of imaging an entire glass slide, the field ofdigital pathology has exploded and is currently regarded as one of themost promising avenues of diagnostic medicine in order to achieve evenbetter, faster, and cheaper diagnosis, prognosis, and prediction ofimportant diseases, such as cancer.

Glass slides that are processed by a digital slide scanning apparatusare very fragile and highly valuable. Glass slides may be stored in avariety of different types of slide racks that are made by differentmanufacturers. The characteristics of an individual slide rack, made bya first manufacturer, can significantly vary from the characteristics ofan individual slide rack, made by a second manufacturer. This causesconventional digital slide scanners to damage glass slides. Therefore,what is needed is a system and method that overcomes these significantproblems found in the conventional systems described above.

SUMMARY

Accordingly, in an embodiment, a slide rack determination system isdescribed herein that operates within a digital slide scanning apparatusand confirms both the type and orientation of a slide rack, holding aplurality of glass slides, prior to scanning the individual glass slideson a scanning stage of the digital slide scanning apparatus. The systemmay include a slide rack clamp apparatus having a lower clamp and anupper clamp. The lower clamp engages a bottom surface of the slide rack.The lower clamp and slide rack are then driven towards the upper clampuntil the upper clamp is engaged with a top surface of the slide rack.The lower clamp and slide rack are driven at a known (e.g., constant)rate, and consequently the time it takes for the upper clamp to engagethe top surface of the slide rack provides an indication as to theheight of the slide rack.

In an embodiment, the upper clamp comprises a plurality of sensors. Thesensors on the upper clamp may be positioned to sense uniquecharacteristics of slide racks from a given manufacturer. Accordingly,when the upper clamp engages the top surface of the slide rack, theindividual sensor that is triggered, or the specific combination ofsensors that are triggered, provide an indication as to the manufacturerof the slide rack and also provides an indication as to the orientationof the slide rack. Notably, many individual slide racks are strikinglyuniform, and therefore it is not uncommon for a slide rack to beprocessed upside down. However, for digital slide scanning purposes,glass slides need to be processed topside-up. Thus, advantageously, theslide rack determination system may be configured to determine anupside-down orientation of a slide rack and generate an alert that willresult in the slide rack not being processed by the digital slidescanning apparatus.

In an embodiment, a slide rack determination system is disclosed thatcomprises: a slide rack engagement surface configured to engage anengagement surface of a slide rack during processing of a slide rack bya digital slide scanning apparatus; one or more sensors configured tosense at least one feature of the slide rack while the engagementsurface of the slide rack is engaged with the slide rack engagementsurface; and at least one hardware processor configured to receive anoutput from the one or more sensors, and, based on the received output,identify the slide rack. Identification of the slide rack may compriseidentifying a manufacturer of the slide rack, identifying a model of theslide rack, and/or determining whether or not usage of the slide rack issupported by the digital slide scanning apparatus.

The at least one hardware processor may be configured to, based on thereceived output, determine an orientation of the slide rack. Inaddition, the at least one hardware processor may be configured to:based on the received output from the one or more sensors, determinewhether or not the orientation of the slide rack is improper; and, whenthe orientation of the slide rack is determined to be improper, initiatean alarm to alert an operator that the orientation of the slide rack isimproper. The orientation of the slide rack may be determined to beimproper when the orientation of the slide rack is upside-down.

In an embodiment, the slide rack determination system further comprisesa motor configured to drive the slide rack along a linear axis withinthe digital slide scanning apparatus towards the slide rack engagementsurface, wherein at least one of the one or more sensors is configuredto sense an engagement between the slide rack engagement surface and theengagement surface of the slide rack, and wherein the at least onehardware processor is further configured to activate the motor, and,based on an output from the at least one sensor, deactivate the motor.The at least one hardware processor may be configured to: determine atime period between activation of the motor and the engagement betweenthe slide rack engagement surface and the engagement surface of theslide rack; and determine a height of the slide rack based on the timeperiod; wherein the identification of the slide rack is further based onthe determined height of the slide rack.

The at least one feature may comprise a feature on a side of the sliderack, wherein the side is orthogonal to the engagement surface of theslide rack. Alternatively or additionally, the at least one feature maycomprise a feature on a peripheral edge of the engagement surface of theslide rack. The one or more sensors may comprise a plurality of sensorsconfigured to sense a plurality of features of the slide rack, whereinthe output from the plurality of sensors comprises indications of theplurality of features, and wherein identifying the slide rack based onthe received output from the plurality of sensors comprises identifyinga slide rack that uniquely corresponds to all of the indications of theplurality of features.

In an embodiment, the slide rack determination system is comprised in adigital slide scanning apparatus. In such an embodiment, the at leastone hardware processor may be configured to control an operation of ascanning process in the digital slide scanning apparatus based on theidentification of the slide rack.

In an embodiment, a method is disclosed that comprises, by at least onehardware processor of a digital slide scanning apparatus: receivingoutput from one or more sensors configured to sense at least one featureof a slide rack while an engagement surface of the slide rack is engagedwith a slide rack engagement surface of the digital slide scanningapparatus; and, based on the received output from the one or moresensors, identify the slide rack.

Other features and advantages of the present invention will become morereadily apparent to those of ordinary skill in the art after reviewingthe following detailed description and accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

The structure and operation of the present invention will be understoodfrom a review of the following detailed description and the accompanyingdrawings in which like reference numerals refer to like parts and inwhich:

FIG. 1A is a top-view diagram illustrating an example slide rack withglass slides from a first manufacturer, according to an embodiment;

FIG. 1B is a top-view diagram illustrating an example slide rack withglass slides from a second manufacturer, according to an embodiment;

FIG. 2A is a perspective-view diagram illustrating an example slide rackfrom a first manufacturer engaged with an upper clamp, according to anembodiment;

FIG. 2B is a perspective-view diagram illustrating an example slide rackfrom a second manufacturer engaged with an upper clamp, according to anembodiment;

FIG. 3 is a flowchart illustrating an example process for identifyingthe presence, orientation, features, manufacturer, and/or model of aslide rack, according to an embodiment;

FIG. 4A is a block diagram illustrating an example processor-enableddevice that may be used in connection with various embodiments describedherein;

FIG. 4B is a block diagram illustrating an example line scan camerahaving a single linear array, according to an embodiment;

FIG. 4C is a block diagram illustrating an example line scan camerahaving three linear arrays, according to an embodiment; and

FIG. 4D is a block diagram illustrating an example line scan camerahaving a plurality of linear arrays, according to an embodiment.

DETAILED DESCRIPTION

Certain embodiments disclosed herein provide for a slide rackdetermination system that determines the height and/or other features,manufacturer and/or model, and/or orientation of a slide rack beingprocessed by a digital slide scanning apparatus. After reading thisdescription it will become apparent to one skilled in the art how toimplement the invention in various alternative embodiments andalternative applications. However, although various embodiments of thepresent invention will be described herein, it is understood that theseembodiments are presented by way of example only, and not limitation. Assuch, this detailed description of various alternative embodimentsshould not be construed to limit the scope or breadth of the presentinvention as set forth in the appended claims.

1. Example Slide Rack Determination System

FIG. 1A is a top-view diagram illustrating an example slide rack 100Afrom a first manufacturer with glass slides 585, according to anembodiment. In the illustrated embodiment, the slide rack 100A comprisesone or more slide rack features 120A-120E that are capable of beingdetected by a sensor, including two recesses 120A and 120B in the topsurface 110A of the slide rack 100A.

FIG. 1B is a top-view diagram illustrating an example slide rack 100Bfrom a second manufacturer with glass slides 585, according to anembodiment. In the illustrated embodiment, the slide rack 100B comprisesone or more slide rack features 120F-120J that are capable of beingdetected by a sensor, including a single recess 120F in the top surface110B of the slide rack 100B.

A slide rack feature 120 may comprise a bump or other protrusion from asurface of the slide rack 100 at a particular location, a notch,opening, or other recess in a surface of the slide rack 100 at aparticular location, the presence of a surface of the slide rack 100 ata particular location, the absence of a surface of the slide rack 100 ata particular location, and/or the like. In an embodiment, a single sliderack feature 120 may be used to uniquely identify a particular sliderack 100. Alternatively, a combination of a plurality of slide rackfeatures 120 may be used, collectively, to uniquely identify aparticular slide rack 100. Since a significant portion of the topsurface 110 of the slide rack 100 may be covered when the slide rack 100is engaged with a slide rack engagement surface of a clamp (e.g., upperclamp 200), it is preferable to use slide rack features 120 that are ona side of the slide rack 100 or near a perimeter edge of the top surface110 of the slide rack 100 for easier detection.

FIG. 2A is a perspective-view diagram illustrating the example sliderack 100A from a first manufacturer, engaged with a slide rackengagement surface (e.g., bottom surface) of an upper clamp 200,according to an embodiment. Similarly, FIG. 2B is a perspective-viewdiagram illustrating the example slide rack 100B from a secondmanufacturer, engaged with the slide rack engagement surface of theupper clamp 200, according to an embodiment.

Attached to the upper clamp 200 are a plurality of sensors 210 and 220.The plurality of sensors may include one or more slide rack orientationsensors 210 and one or more slide rack feature sensors 220. In theillustrated embodiment, the plurality of sensors include a single sliderack orientation sensor 210 and two slide rack feature sensors 220A and220B. In addition, at least one of the plurality of sensors 210 and/or220 and/or another sensor may be configured to determine whether or notthe slide rack 100 is engaged with the slide rack engagement surface ofthe upper clamp 200. In alternative embodiments, additional or fewersensors may be employed.

In an embodiment, each slide rack orientation sensor 210 is configuredto sense a slide rack feature 120 that indicates whether the slide rack100 is topside-up or upside-down. Each slide rack orientation sensor 210may be specific to a single type of slide rack 100 (e.g., 100A) or maybe configured to determine the orientation of two or more types of slideracks 100 (e.g., 100A and 100B).

In an embodiment, each slide rack feature sensor 220 is configured todetermine the presence or absence of at least one slide rack feature120. In an embodiment which identifies a manufacturer and/or model ofthe slide rack 100 based on a plurality of slide rack features 120, twoor more slide rack feature sensors 220 (e.g., 220A and 220B in theillustrated embodiment) may be used to determine which of a plurality ofmanufacturers manufactured the slide rack 100 and/or which of aplurality of models is present. Specifically, the combined outputs ofthe slide rack feature sensors 220, each representing the presence orabsence of a particular slide rack feature 120 and/or one or moreparameters (e.g., height, width, depth, thickness, shape, diameter,etc.) of a particular slide rack feature 120, may be used to uniquelyidentify each manufacturer's slide racks 100 and/or each model of sliderack 100. For example, the presence of a first slide rack feature 120(e.g., 120E) and/or absence of a second slide rack feature 120 (e.g.,120H) may indicate that the slide rack 100A from the first manufactureris present, whereas the absence of the first slide rack feature 120and/or presence of the second slide rack feature 120 may indicate thatthe slide rack 100B from the second manufacturer is present.

In an embodiment, the digital slide scanning apparatus comprises aprocessor 555, which monitors each output of slide rack orientationsensor(s) 210 during slide processing, and analyzes the output(s) todetermine the orientation of the slide rack 100 based on the output ofslide rack orientation sensor(s) 210. In the event that thedetermination is performed based on the outputs from a plurality ofslide rack orientation sensors 210, the processor 555 monitors theplurality of outputs from these slide rack orientation sensors 210before and/or during slide processing. During monitoring, if theprocessor 555 determines that the position of the slide rack 100 hasbecome abnormal based on the output(s) of the slide rack orientationsensor(s) 210, the processor 555 may trigger an alarm (e.g., an audioalert via a speaker of the digital slide scanning apparatus and/or avisual alert via a display or light source of the digital slide scanningapparatus) to warn an operator of the digital slide scanning apparatusthat the slide rack 100 is abnormally positioned. The processor 555 mayalso halt any slide processing until the slide rack 100 is repositioned,such that the processor 555 determines, based on the output(s) of theslide rack orientation sensor(s) 210, that the slide rack 100 isproperly positioned.

Additionally or alternatively, the processor 555 of the digital slidescanning apparatus receives each output of slide rack feature sensor(s)220, and analyzes the output(s) to determine the presence or absence ofa slide rack 100 and/or, if the slide rack 100 is determined to bepresent, uniquely identify the manufacturer, model, and/or other type ofthe slide rack 100 and/or determine whether or not usage of the sliderack 100 is supported by the digital slide scanning apparatus. If theprocessor 555 determines that usage of the slide rack 100 is notsupported by the digital slide scanning apparatus, the processor 555 mayprevent any slide processing, so as to prevent potential damage to glassslides 585 within the slide rack 100, the slide rack 100, and/or thedigital slide scanning apparatus.

2. Example Slide Rack Determination Process

FIG. 3 is a flowchart that illustrates a process 300 for identifying thepresence, orientation, features, manufacturer, and/or model of a sliderack 100, according to an embodiment. While the process 300 isillustrated with a certain arrangement and ordering of steps, theprocess 300 may be implemented with fewer, more, or different steps anda different arrangement and/or ordering of steps. The process 300 may beimplemented by the processor 555 of a digital slide scanning apparatus,such as the scanning system 550 illustrated in FIG. 4A.

The process 300 begins in step 310, when a motor begins driving theslide rack 100, such that the engagement surface 110 (e.g., top surface)of the slide rack 100 moves toward the slide rack engagement surface(e.g., bottom surface) of the clamp 200. For instance, anotherengagement surface (e.g., bottom surface) of the slide rack 100 may reston a slide rack engagement surface (e.g., top surface) of a lower clamp.The lower clamp may comprise a sensor that detects the presence of theslide rack 100, and the processor 555 may automatically activate themotor to drive the lower clamp towards the upper clamp 200 whenever thesensor detects the presence of the slide rack 100. Alternatively, anoperator may manually activate the motor, under the control of theprocessor 555, to drive the lower clamp towards the upper clamp 200.

In addition, in step 310, the processor 555 may start monitoring a timefrom the activation time of the motor until an engagement time at whichthe engagement surface 110 of the slide rack 100 engages the slide rackengagement surface of the upper clamp 200. For example, the processor555 may start a timer at the activation time to be stopped at theengagement time. Alternatively, the processor 555 may store anactivation time at which the motor was activated and continually comparethat activation time to a current time (e.g., until the engagementtime).

In step 320, the processor 555 monitors an output of an engagementsensor (e.g., sensor 210, 220, or another sensor) of upper clamp 200. Ifthe engagement sensor detects the slide rack 100, it outputs a detectionindication to the processor 555. Otherwise, if the engagement sensordoes not detect the slide rack, it outputs no indication or anon-detection indication to the processor 555. If the processor 555receives the detection indication (i.e., “YES” in step 320), the process300 proceeds to step 350. Otherwise, if the processor 555 does notreceive the detection indication or receives a non-detection indication(i.e., “NO” in step 320), the process 300 proceeds to step 330.

In step 330, the processor 555 determines whether or not the timeperiod, from the activation time in step 310 to the current time, isgreater than a threshold value. The threshold value may be set to alength of time that is indicative of the absence of any slide rack 100between the upper and lower clamps or indicative of another error. Ifthe length of time is greater than the threshold value (i.e., “YES” instep 330), the processor 555 may issue an alarm in step 340 (e.g., anaudio and/or visual alert) to notify an operator that an error wasencountered. The alarm may comprise an indication of the error (e.g.,the absence of a slide rack 100). Otherwise, if the length of time isnot greater than the threshold value (i.e., “NO” in step 330), theprocess 300 may continue to monitor for engagement in step 320. Itshould be understood that if the length of time is equal to thethreshold value, the processor 555 may issue an alarm or continue tostep 320, depending on the programmer's particular design choice.

In an alternative embodiment, the processor 555 may utilize other meansfor detecting the absence of the slide rack 100. In such a case, step310 could omit the start of the engagement timing and step 330 could beomitted entirely. As an example, the absence of the slide rack 100 couldbe detected by sensing that the engagement surface of the lower clamp iswithin a predetermined distance from the engagement surface of the upperclamp or has reached the engagement surface of the upper clamp.

In step 350, the processor 555 may determine the height of the sliderack 100. In an embodiment, the height of the slide rack 100 iscalculated based on the time period from the activation time in step 310to the engagement time detected in step 320. For example, the height ofthe slide rack 100 could be calculated based on the time period and aknown constant speed of the motor activated in step 310 (e.g.,height=speed×time period). Alternatively, the height of the slide rack100 could be determined based on a distance between the lower clamp andupper clamp 200 at the time of the engagement detected in step 320. Itshould be understood that the height of the slide rack 100 may beutilized as a feature for identifying the manufacturer and/or model ofthe slide rack 100. In an embodiment in which the height of the sliderack 100 is not required to identify the manufacturer of the slide rack100, step 350 could be omitted.

In step 360, the processor 55 may determine the orientation of the sliderack 100. For example, the processor 555 may receive an output from oneor more slide rack orientation sensors 210. Based on the output from theslide rack orientation sensor(s) 210, the processor may determine theorientation of the slide rack 100. For example, the processor maydetermine whether the slide rack 100 is topside-up or upside-down.

In step 370, if the orientation of the slide rack 100 is incorrect orimproper (i.e., “NO” in step 370), the processor 555 may issue an alarmin step 340. For example, an incorrect or improper orientation maycomprise an upside-down orientation of the slide rack 100. The alarm maycomprise an indication of the error (e.g., improper orientation of theslide rack 100). Otherwise, if the orientation of the slide rack 100 iscorrect and proper (i.e., “YES” in step 370), the process 300 proceedsto step 380.

In step 380, the processor 555 may detect one or more features of theslide rack 100. For example, the processor 555 may receive an outputfrom one or more slide rack feature sensors 220. Based on the outputfrom the slide rack feature sensor(s) 220 and/or other detected features(e.g., the height of the slide rack determined in step 350), theprocessor 555 may identify the slide rack 100 in step 390.

Specifically, in step 390, the processor 555 may identify themanufacturer and/or model of the slide rack 100. This identification maythen be used for further processing by the digital slide scanningapparatus 550. For example, the identity of the manufacturer and/ormodel of the slide rack 100 may be used to determine whether or not theslide rack 100 is supported by the digital slide scanning apparatus 550,to configure an operation of the digital slide scanning apparatus 550,such as controlling the operation of an assembly for loading andunloading slides 585 from the slide rack 100, and/or the like.

3. Example Embodiments

In an embodiment, a slide rack determination system includes a sliderack engagement surface configured to engage a top surface of a sliderack during processing of a slide rack by a digital slide scanningapparatus. The slide rack determination system also includes at leastone sensor configured to sense at least one feature of the slide rackwhen the slide rack is engaged with the slide rack engagement surface.The slide rack determination system also includes a processor configuredto receive one or more indications from the at least one sensor andanalyze the received one or more indications to determine a manufacturerof the slide rack.

In an embodiment, a slide rack determination system includes a sliderack engagement surface configured to engage a top surface of a sliderack during processing of a slide rack by a digital slide scanningapparatus. The slide rack determination system also includes at leastone sensor configured to sense at least one feature of the slide rackwhen the slide rack is engaged with the slide rack engagement surface.The slide rack determination system also includes a processor configuredto receive one or more indications from the at least one sensor andanalyze the received one or more indications to determine an orientationof the slide rack.

In an embodiment, a slide rack determination system includes a motorconfigured to drive a slide rack along a linear axis within a digitalslide scanning apparatus, wherein the motor begins driving the sliderack at a first time. The slide rack determination system also includesa slide rack engagement surface positioned along the linear axis andconfigured to engage a top surface of the slide rack during processingof a slide rack by the digital slide scanning apparatus. The slide rackdetermination system also includes at least one sensor configured tosense the engagement of the slide rack and the slide rack engagementsurface, wherein the slide rack engages the slide rack engagementsurface at a second time. The slide rack determination system alsoincludes a processor configured to drive the motor, the processorfurther configured to determine the first time based on a start time ofdriving the motor, the processor further configured to receive anindication from the at least one sensor confirming the engagement of theslide rack and the slide rack engagement surface, the processor furtherconfigured to determine the second time based on the receivedindication, and the processor further configured to determine a heightof the slide rack based on the first time and the second time.Similarly, the processor may determine an absence of a slide rack basedon an elapsed amount of time after the first time, such that if theprocessor drives the motor longer than a predetermined amount of time,the processor determines the absence of a slide rack.

In an embodiment, a slide rack determination method includes driving aslide rack toward a slide rack engagement surface comprising a pluralityof sensors, and, subsequent to engaging a top surface of the slide rackwith the slide rack engagement surface, receiving an indication from theone or more sensors. The method also includes analyzing the indicationfrom the one or more sensors and determining a slide rack manufacturerbased on the analysis.

In an embodiment, a slide rack determination method includes driving aslide rack toward a slide rack engagement surface comprising a pluralityof sensors, and, subsequent to engaging a top surface of the slide rackwith the slide rack engagement surface, receiving an indication from theone or more sensors. The method also includes analyzing the indicationfrom the one or more sensors and determining a slide rack orientationbased on the analysis.

In an embodiment, a method includes using a motor to drive a slide racktoward a slide rack engagement surface comprising a plurality ofsensors, and storing a first time corresponding to when the motorstarted driving the slide rack. The method also includes sensing anengagement of the slide rack with the slide rack engagement surface, andstoring a second time corresponding to when the slide rack engaged withthe slide rack engagement surface, and determining a slide rack heightbased on the analysis.

4. Example Digital Slide Scanning Apparatus

FIG. 4A is a block diagram illustrating an example processor-enableddevice 550 that may be used in connection with various embodimentsdescribed herein. Alternative forms of the device 550 may also be usedas will be understood by the skilled artisan. In the illustratedembodiment, the device 550 is presented as a digital imaging device(also referred to as a digital slide scanning apparatus, digital slidescanner, scanner, scanner system, digital imaging device, etc.) thatcomprises one or more processors 555, one or more memories 565, one ormore motion controllers 570, one or more interface systems 575, one ormore movable stages 580 that each support one or more glass slides 585with one or more samples 590, one or more illumination systems 595 thatilluminate the sample, one or more objective lenses 600 that each definean optical path 605 that travels along an optical axis, one or moreobjective lens positioners 630, one or more optional epi-illuminationsystems 635 (e.g., included in a fluorescence scanner system), one ormore focusing optics 610, one or more line scan cameras 615 and/or oneor more area scan cameras 620, each of which define a separate field ofview 625 on the sample 590 and/or glass slide 585. The various elementsof the scanner system 550 are communicatively coupled via one or morecommunication busses 560. Although there may be one or more of each ofthe various elements of the scanner system 550, for simplicity in thedescription, these elements will be described in the singular exceptwhen needed to be described in the plural to convey the appropriateinformation.

The one or more processors 555 may include, for example, a centralprocessing unit (CPU) and a separate graphics processing unit (GPU)capable of processing instructions in parallel, or the one or moreprocessors 555 may include a multi-core processor capable of processinginstructions in parallel. Additional separate processors may also beprovided to control particular components or perform particularfunctions such as image processing. For example, additional processorsmay include an auxiliary processor to manage data input, an auxiliaryprocessor to perform floating point mathematical operations, aspecial-purpose processor having an architecture suitable for fastexecution of signal processing algorithms (e.g., digital-signalprocessor), a slave processor subordinate to the main processor (e.g.,back-end processor), an additional processor for controlling the linescan camera 615, the stage 580, the objective lens 225, and/or a display(not shown). Such additional processors may be separate discreteprocessors or may be integrated with the processor 555. The one or moreprocessors may be configured to control the motor that drives the lowerclamp and further configured to receive indications from the one or moresensors attached to the upper clamp 200, and thereby control the overallworkflow of the digital imaging device 550 and determine the height,manufacturer, and/or orientation of a slide rack 100 being processed bythe digital imaging device 550.

The memory 565 provides storage of data and instructions for programsthat can be executed by the processor 555. The memory 565 may includeone or more volatile and/or non-volatile computer-readable storagemediums that store the data and instructions, including, for example, arandom access memory, a read only memory, a hard disk drive, a removablestorage drive, and/or the like. The processor 555 is configured toexecute instructions that are stored in memory 565 and communicate viacommunication bus 560 with the various elements of the scanner system550 to carry out the overall function of the scanner system 550.

The one or more communication busses 560 may include a communication bus560 that is configured to convey analog electrical signals and mayinclude a communication bus 560 that is configured to convey digitaldata. Accordingly, communications from the processor 555, the motioncontroller 570, and/or the interface system 575, via the one or morecommunication busses 560, may include both electrical signals anddigital data. The processor 555, the motion controller 570, and/or theinterface system 575 may also be configured to communicate with one ormore of the various elements of the scanning system 550 via a wirelesscommunication link.

The motion control system 570 is configured to precisely control andcoordinate X-Y-Z movement of the stage 580 and the objective lens 600(e.g., via the objective lens positioner 630). The motion control system570 is also configured to control movement of any other moving part inthe scanner system 550. For example, in a fluorescence scannerembodiment, the motion control system 570 is configured to coordinatemovement of optical filters and the like in the epi-illumination system635.

The interface system 575 allows the scanner system 550 to interface withother systems and human operators. For example, the interface system 575may include a user interface to provide information directly to anoperator and/or to allow direct input from an operator. The interfacesystem 575 is also configured to facilitate communication and datatransfer between the scanning system 550 and one or more externaldevices that are directly connected (e.g., a printer, removable storagemedium, etc.) or external devices, such as an image server system, anoperator station, a user station, and an administrative server system,that are connected to the scanner system 550 via a network (not shown).

The illumination system 595 is configured to illuminate a portion of thesample 590. The illumination system 595 may include, for example, alight source and illumination optics. The light source could be avariable intensity halogen light source with a concave reflective mirrorto maximize light output and a KG-1 filter to suppress heat. The lightsource could also be any type of arc-lamp, laser, or other source oflight. In an embodiment, the illumination system 595 illuminates thesample 590 in transmission mode such that the line scan camera 615and/or area scan camera 620 sense optical energy that is transmittedthrough the sample 590. Alternatively or additionally, the illuminationsystem 595 may be configured to illuminate the sample 590 in reflectionmode such that the line scan camera 615 and/or area scan camera 620sense optical energy that is reflected from the sample 590. Overall, theillumination system 595 is configured to be suitable for interrogationof the microscopic sample 590 in any known mode of optical microscopy.

In an embodiment, the scanner system 550 optionally includes anepi-illumination system 635 to optimize the scanner system 550 forfluorescence scanning. Fluorescence scanning is the scanning of samples590 that include fluorescence molecules, which are photon sensitivemolecules that can absorb light at a specific wavelength (excitation).These photon sensitive molecules also emit light at a higher wavelength(emission). Because the efficiency of this photoluminescence phenomenonis very low, the amount of emitted light is often very low. This lowamount of emitted light typically frustrates conventional techniques forscanning and digitizing the sample 590 (e.g., transmission modemicroscopy). Advantageously, in an optional fluorescence scanner systemembodiment of the scanner system 550, use of a line scan camera 615 thatincludes multiple linear sensor arrays (e.g., a time delay integration(TDI) line scan camera) increases the sensitivity to light of the linescan camera by exposing the same area of the sample 590 to each of themultiple linear sensor arrays of the line scan camera 615. This isparticularly useful when scanning faint fluorescence samples with lowemitted light.

Accordingly, in a fluorescence scanner system embodiment, the line scancamera 615 is preferably a monochrome TDI line scan camera.Advantageously, monochrome images are ideal in fluorescence microscopybecause they provide a more accurate representation of the actualsignals from the various channels present on the sample. As will beunderstood by those skilled in the art, a fluorescence sample 590 can belabeled with multiple florescence dyes that emit light at differentwavelengths, which are also referred to as “channels.”

Furthermore, because the low and high end signal levels of variousfluorescence samples present a wide spectrum of wavelengths for the linescan camera 615 to sense, it is desirable for the low and high endsignal levels that the line scan camera 615 can sense to be similarlywide. Accordingly, in a fluorescence scanner embodiment, a line scancamera 615 used in the fluorescence scanning system 550 is a monochrome10-bit 64-linear-array TDI line scan camera. It should be noted that avariety of bit depths for the line scan camera 615 can be employed foruse with a fluorescence scanner embodiment of the scanning system 550.

The movable stage 580 is configured for precise X-Y axes movement undercontrol of the processor 555 or the motion controller 570. The movablestage may also be configured for movement in a Z axis under control ofthe processor 555 or the motion controller 570. The moveable stage isconfigured to position the sample in a desired location during imagedata capture by the line scan camera 615 and/or the area scan camera.The moveable stage is also configured to accelerate the sample 590 in ascanning direction to a substantially constant velocity and thenmaintain the substantially constant velocity during image data captureby the line scan camera 615. In an embodiment, the scanner system 550may employ a high-precision and tightly coordinated X-Y grid to aid inthe location of the sample 590 on the movable stage 580. In anembodiment, the movable stage 580 is a linear motor based X-Y stage withhigh precision encoders employed on both the X and the Y axes. Forexample, very precise nanometer encoders can be used on the axis in thescanning direction and on the axis that is in the directionperpendicular to the scanning direction and on the same plane as thescanning direction. The stage is also configured to support the glassslide 585 upon which the sample 590 is disposed.

The sample 590 can be anything that may be interrogated by opticalmicroscopy. For example, a glass microscope slide 585 is frequently usedas a viewing substrate for specimens that include tissues and cells,chromosomes, DNA, protein, blood, bone marrow, urine, bacteria, beads,biopsy materials, or any other type of biological material or substancethat is either dead or alive, stained or unstained, labeled orunlabeled. The sample 590 may also be an array of any type of DNA orDNA-related material such as cDNA, RNA, or protein that is deposited onany type of slide or other substrate, including any and all samplescommonly known as microarrays. The sample 590 may be a microtiter plate,for example a 96-well plate. Other examples of the sample 590 includeintegrated circuit boards, electrophoresis records, petri dishes, film,semiconductor materials, forensic materials, and machined parts.

Objective lens 600 is mounted on the objective positioner 630 which, inan embodiment, may employ a very precise linear motor to move theobjective lens 600 along the optical axis defined by the objective lens600. For example, the linear motor of the objective lens positioner 630may include a 50 nanometer encoder. The relative positions of the stage580 and the objective lens 600 in X-Y-Z axes are coordinated andcontrolled in a closed loop manner using motion controller 570 under thecontrol of the processor 555 that employs memory 565 for storinginformation and instructions, including the computer-executableprogrammed steps for overall operation of the scanning system 550.

In an embodiment, the objective lens 600 is a plan apochromatic (“APO”)infinity-corrected objective with a numerical aperture corresponding tothe highest spatial resolution desirable, where the objective lens 600is suitable for transmission mode illumination microscopy, reflectionmode illumination microscopy, and/or epi-illumination mode fluorescencemicroscopy (e.g., an Olympus 40×, 0.75NA or 20×, 0.75 NA).Advantageously, objective lens 600 is capable of correcting forchromatic and spherical aberrations. Because objective lens 600 isinfinity corrected, focusing optics 610 can be placed in the opticalpath 605 above the objective lens 600 where the light beam passingthrough the objective lens becomes a collimated light beam. The focusingoptics 610 focus the optical signal captured by the objective lens 600onto the light-responsive elements of the line scan camera 615 and/orthe area scan camera 620 and may include optical components such asfilters, magnification changer lenses, and/or the like. The objectivelens 600 combined with focusing optics 610 provides the totalmagnification for the scanning system 550. In an embodiment, thefocusing optics 610 may contain a tube lens and an optional 2×magnification changer. Advantageously, the 2× magnification changerallows a native 20× objective lens 600 to scan the sample 590 at 40×magnification.

The line scan camera 615 comprises at least one linear array of pictureelements (“pixels”). The line scan camera may be monochrome or color.Color line scan cameras typically have at least three linear arrays,while monochrome line scan cameras may have a single linear array orplural linear arrays. Any type of singular or plural linear array,whether packaged as part of a camera or custom-integrated into animaging electronic module, can also be used. For example, a3-linear-array (“red-green-blue” or “RGB”) color line scan camera or a96-linear-array monochrome TDI may also be used. TDI line scan camerastypically provide a substantially better signal-to-noise ratio (SNR) inthe output signal by summing intensity data from previously imagedregions of a specimen, yielding an increase in the SNR that is inproportion to the square-root of the number of integration stages. TDIline scan cameras comprise multiple linear arrays. For example, TDI linescan cameras are available with 24, 32, 48, 64, 96, or even more lineararrays. The scanner system 550 also supports linear arrays that aremanufactured in a variety of formats including some with 512 pixels,some with 1,024 pixels, and others having as many as 4,096 pixels.Similarly, linear arrays with a variety of pixel sizes can also be usedin the scanner system 550. The salient requirement for the selection ofany type of line scan camera 615 is that the motion of the stage 580 canbe synchronized with the line rate of the line scan camera 615, so thatthe stage 580 can be in motion with respect to the line scan camera 615during the digital image capture of the sample 590.

The image data generated by the line scan camera 615 is stored in aportion of the memory 565 and processed by the processor 555 to generatea contiguous digital image of at least a portion of the sample 590. Thecontiguous digital image can be further processed by the processor 555,and the processed contiguous digital image can also be stored in thememory 565.

In an embodiment with two or more line scan cameras 615, at least one ofthe line scan cameras 615 can be configured to function as a focusingsensor that operates in combination with at least one of the line scancameras 615 that is configured to function as an imaging sensor. Thefocusing sensor can be logically positioned on the same optical axis asthe imaging sensor, or the focusing sensor may be logically positionedbefore or after the imaging sensor with respect to the scanningdirection of the scanner system 550. In an embodiment with at least oneline scan camera 615 functioning as a focusing sensor, the image datagenerated by the focusing sensor is stored in a portion of the memory565 and processed by the one or more processors 555 to generate focusinformation to allow the scanner system 550 to adjust the relativedistance between the sample 590 and the objective lens 600 to maintainfocus on the sample during scanning. Additionally, in an embodiment, theat least one line scan camera 615 functioning as a focusing sensor maybe oriented such that each of a plurality of individual pixels of thefocusing sensor is positioned at a different logical height along theoptical path 605.

In operation, the various components of the scanner system 550 and theprogrammed modules stored in memory 565 enable automatic scanning anddigitizing of the sample 590, which is disposed on a glass slide 585.The glass slide 585 is securely placed on the movable stage 580 of thescanner system 550 for scanning the sample 590. Under control of theprocessor 555, the movable stage 580 accelerates the sample 590 to asubstantially constant velocity for sensing by the line scan camera 615,where the speed of the stage is synchronized with the line rate of theline scan camera 615. After scanning a stripe of image data, the movablestage 580 decelerates and brings the sample 590 to a substantiallycomplete stop. The movable stage 580 then moves orthogonal to thescanning direction to position the sample 590 for scanning of asubsequent stripe of image data (e.g., an adjacent stripe). Additionalstripes are subsequently scanned until an entire portion of the sample590 or the entire sample 590 is scanned.

For example, during digital scanning of the sample 590, a contiguousdigital image of the sample 590 is acquired as a plurality of contiguousfields of view that are combined together to form an image stripe. Aplurality of adjacent image stripes are similarly combined together toform a contiguous digital image of a portion of the sample 590 or theentire sample 590. The scanning of the sample 590 may include acquiringvertical image stripes or horizontal image stripes. The scanning of thesample 590 may be either top-to-bottom, bottom-to-top, or both(bi-directional) and may start at any point on the sample.Alternatively, the scanning of the sample 590 may be eitherleft-to-right, right-to-left, or both (bi-directional) and may start atany point on the sample. Additionally, it is not necessary that imagestripes be acquired in an adjacent or contiguous manner. Furthermore,the resulting image of the sample 590 may be an image of the entiresample 590 or only a portion of the sample 590.

In an embodiment, computer-executable instructions (e.g., programmedmodules or other software) are stored in the memory 565 and, whenexecuted, enable the scanning system 550 to perform the variousfunctions described herein. In this description, the term“computer-readable storage medium” is used to refer to any media used tostore and provide computer executable instructions to the scanningsystem 550 for execution by the processor 555. Examples of these mediainclude memory 565 and any removable or external storage medium (notshown) communicatively coupled with the scanning system 550 eitherdirectly or indirectly (e.g., via a network).

FIG. 4B illustrates a line scan camera having a single linear array 640,which may be implemented as a charge coupled device (“CCD”) array. Thesingle linear array 640 comprises a plurality of individual pixels 645.In the illustrated embodiment, the single linear array 640 has 4,096pixels. In alternative embodiments, linear array 640 may have more orfewer pixels. For example, common formats of linear arrays include 512,1,024, and 4,096 pixels. The pixels 645 are arranged in a linear fashionto define a field of view 625 for the linear array 640. The size of thefield of view varies in accordance with the magnification of the scannersystem 550.

FIG. 4C illustrates a line scan camera having three linear arrays, eachof which may be implemented as a CCD array. The three linear arrayscombine to form a color array 650. In an embodiment, each individuallinear array in the color array 650 detects a different color intensity(e.g., red, green, or blue). The color image data from each individuallinear array in the color array 650 is combined to form a single fieldof view 625 of color image data.

FIG. 4D illustrates a line scan camera having a plurality of lineararrays, each of which may be implemented as a CCD array. The pluralityof linear arrays combine to form a TDI array 655. Advantageously, a TDIline scan camera may provide a substantially better SNR in its outputsignal by summing intensity data from previously imaged regions of aspecimen, yielding an increase in the SNR that is in proportion to thesquare root of the number of linear arrays (also referred to asintegration stages). A TDI line scan camera may comprise a largervariety of numbers of linear arrays. For example, common formats of TDIline scan cameras include 24, 32, 48, 64, 96, 120 and even more lineararrays.

The above description of the disclosed embodiments is provided to enableany person skilled in the art to make or use the invention. Variousmodifications to these embodiments will be readily apparent to thoseskilled in the art, and the generic principles described herein can beapplied to other embodiments without departing from the spirit or scopeof the invention. Thus, it is to be understood that the description anddrawings presented herein represent a presently preferred embodiment ofthe invention and are therefore representative of the subject matterwhich is broadly contemplated by the present invention. It is furtherunderstood that the scope of the present invention fully encompassesother embodiments that may become obvious to those skilled in the artand that the scope of the present invention is accordingly not limited.

What is claimed is:
 1. A slide rack determination system, comprising: aslide rack engagement surface configured to engage an engagement surfaceof a slide rack during processing of a slide rack by a digital slidescanning apparatus; one or more sensors configured to sense at least onefeature of the slide rack while the engagement surface of the slide rackis engaged with the slide rack engagement surface; and at least onehardware processor configured to receive an output from the one or moresensors, and, based on the received output, identify the slide rack. 2.The slide rack determination system of claim 1, wherein identifying theslide rack comprises identifying a manufacturer of the slide rack. 3.The slide rack determination system of claim 1, wherein identifying theslide rack comprises identifying a model of the slide rack.
 4. The sliderack determination system of claim 1, wherein identifying the slide rackcomprises determining whether or not usage of the slide rack issupported by the digital slide scanning apparatus.
 5. The slide rackdetermination system of claim 1, wherein the at least one hardwareprocessor is further configured to, based on the received output,determine an orientation of the slide rack.
 6. The slide rackdetermination system of claim 1, wherein the at least one hardwareprocessor is further configured to: based on the received output fromthe one or more sensors, determine whether or not the orientation of theslide rack is improper; and, when the orientation of the slide rack isdetermined to be improper, initiate an alarm to alert an operator thatthe orientation of the slide rack is improper.
 7. The slide rackdetermination system of claim 6, wherein the orientation of the sliderack is determined to be improper when the orientation of the slide rackis upside-down.
 8. The slide rack determination system of claim 1,further comprising a motor configured to drive the slide rack along alinear axis within the digital slide scanning apparatus towards theslide rack engagement surface, wherein at least one of the one or moresensors is configured to sense an engagement between the slide rackengagement surface and the engagement surface of the slide rack, andwherein the at least one hardware processor is further configured toactivate the motor, and, based on an output from the at least onesensor, deactivate the motor.
 9. The slide rack determination system ofclaim 8, wherein the at least one hardware processor is furtherconfigured to: determine a time period between activation of the motorand the engagement between the slide rack engagement surface and theengagement surface of the slide rack; and determine a height of theslide rack based on the time period; wherein the identification of theslide rack is further based on the determined height of the slide rack.10. The slide rack determination system of claim 1, wherein the at leastone feature comprises a feature on a side of the slide rack, wherein theside is orthogonal to the engagement surface of the slide rack.
 11. Theslide rack determination system of claim 1, wherein the at least onefeature comprises a feature on a peripheral edge of the engagementsurface of the slide rack.
 12. The slide rack determination system ofclaim 1, wherein the one or more sensors comprise a plurality of sensorsconfigured to sense a plurality of features of the slide rack, whereinthe output from the plurality of sensors comprises indications of theplurality of features, and wherein identifying the slide rack based onthe received output from the plurality of sensors comprises identifyinga slide rack that uniquely corresponds to all of the indications of theplurality of features.
 13. A digital slide scanning apparatus comprisingthe slide rack determination system of claim
 1. 14. The digital slidescanning apparatus of claim 13, wherein the at least one hardwareprocessor is further configured to control an operation of a scanningprocess in the digital slide scanning apparatus based on theidentification of the slide rack.
 15. A method comprising, by at leastone hardware processor of a digital slide scanning apparatus: receivingoutput from one or more sensors configured to sense at least one featureof a slide rack while an engagement surface of the slide rack is engagedwith a slide rack engagement surface of the digital slide scanningapparatus; and, based on the received output from the one or moresensors, identify the slide rack.